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Identification of DNA Methyltransferase-1 Inhibitor For molecules Article Identification of DNA Methyltransferase-1 Inhibitor for Breast Cancer Therapy through Computational Fragment-Based Drug Design Ahmad Husein Alkaff , Mutiara Saragih , Shabrina Noor Imana, Mochammad Arfin Fardiansyah Nasution and Usman Sumo Friend Tambunan * Bioinformatics and Biomedicals Research Group, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, West Java, Indonesia; [email protected] (A.H.A.); [email protected] (M.S.); [email protected] (S.N.I.); marfi[email protected] (M.A.F.N.) * Correspondence: [email protected] Abstract: Epimutation by DNA Methyltransferase 1 (DNMT1), an epigenetic regulator enzyme, may lead to the proliferation of breast cancer. In this report, 168,686 natural products from the PubChem database were screened and modified by in silico method to acquire the potential inhibitor of DNMT1. The initial screening of PubChem natural products using Lipinski’s and Veber’s rules of three and toxic properties have resulted in 2601 fragment candidates. Four fragments from pharmacophore-based molecular docking simulation were modified by utilizing FragFP and the Lipinski’s and Veber’s rules of five, and resulted in 51,200 ligands. The toxicological screening collected 13,563 ligands for a series of pharmacophore-based molecular docking simulations to sort out the modified ligands, which had the better binding activity and interactions to DNMT1 compared to the standards, SAH, SAM, and SFG. This step resulted in five ligand candidates, namely C-7756, C-5769, C-1723, C-2129, and C-2140. The ADME-Tox properties prediction showed that the Citation: Alkaff, A.H.; Saragih, M.; selected ligands are generally better than standards in terms of druglikeness, GI absorption, and oral Imana, S.N.; Nasution, M.A.F.; bioavailability. C-7756 exhibited a stronger affinity to DNMT1 as well as better ADME-Tox properties Tambunan, U.S.F. Identification of compared to the other ligands. DNA Methyltransferase-1 Inhibitor for Breast Cancer Therapy through Keywords: dengue; envelope protein; natural product; fragment growing; molecular docking simu- Computational Fragment-Based Drug lation Design. Molecules 2021, 26, 375. http://doi.org/10.3390/ molecules26020375 1. Introduction Academic Editor: Phurpa Wangchuk Received: 26 November 2020 Cancer is a chronic disease characterized by uncontrolled cell growth that can spread Accepted: 10 January 2021 to tissues and other organs in the body [1]. Breast cancer is one type of cancer with many Published: 13 January 2021 cases of death among female patients and continues to be a global medical issue. Even though the number of major medical advances have improved the treatment of primary Publisher’s Note: MDPI stays neu- breast cancer [2], it still contributes to 11.6% of the total cancer incidence burden worldwide, tral with regard to jurisdictional clai- with approximately 2.1 million people suffering from breast cancer in 2018 [3]. In Indonesia, ms in published maps and institutio- breast cancer continues to be the most common malignancy in women, with an incidence nal affiliations. rate of 30.9% per total number of 188,231 new cases in 2018 [4]. DNA Methyltransferase 1 (DNMT1) is an epigenetic regulator enzyme responsible for forming and maintaining DNA methylation patterns [5]. The epigenetic modification through methylation at cytosine residues of DNA plays essential role in regulating gene Copyright: © 2021 by the authors. Li- censee MDPI, Basel, Switzerland. expression without altering the original DNA sequence [6]. The DNMT1 protein consists This article is an open access article of five domains, which are: replication foci targeting sequence (RTFS) domain, CXXC distributed under the terms and con- zinc finger domain, bromo adjacent homology 1 (BAH1) domain, BAH2 domain, and ditions of the Creative Commons At- MTase domains (Figure1)[ 7]. During DNA methylation, the transfer of the adenosyl-L- 0 tribution (CC BY) license (https:// methionine (SAM) methyl group (-CH3) to the 5 -cytosine position in the DNA sequence creativecommons.org/licenses/by/ forming 5-methylcytosine (5mC) and S-adenosyl-L-homocysteine (SAH), occurs in the 4.0/). MTase domain [8]. Molecules 2021, 26, 375. https://doi.org/10.3390/molecules26020375 https://www.mdpi.com/journal/molecules Molecules 2021, 26, x FOR PEER REVIEW 2 of 18 Molecules 2021, 26, 375 5‐methylcytosine (5mC) and S‐adenosyl‐L‐homocysteine (SAH), occurs in the MTase do‐ 2 of 18 main [8]. Figure 1. TheFigure 3D structure 1. The 3D of structure the DNMT1 of the protein DNMT1 (PDB protein ID: 3AV5 (PDB [5]) ID: with 3AV5 the [5 ])RFTS, with CXXC, the RFTS, Mtase, CXXC, Mtase, BAH1, andBAH1, BAH2 domain, and BAH2 which domain, are marked which are in green, marked red, in blue, green, magenta, red, blue, and magenta, orange, and respectively. orange, respectively. The SAH (orangeThe SAH‐colored (orange-colored space‐filling space-filling model) occupies model) a hydrophobic occupies a hydrophobic pocket in the pocket MTase in domain. the MTase domain. In the normalIn the cells, normal epigenetic cells, epigenetic regulation regulation dictates the dictates expression the expression of oncogenes, of oncogenes, which which encourageencourage the formation the formation of cancer ofcells, cancer and cells,tumor and suppressor tumor suppressor genes that genes regulate that the regulate the growth asgrowth well as as the well life as cycle the lifeof a cycle cell. ofEpimutation a cell. Epimutation or epigenetic or epigenetic alteration alteration is a change is a change in in the DNAthe methylation DNA methylation pattern pattern occurring occurring in various in various types of types cancer of cancerwhere wherethere is there a mas is‐ a massive sive upregulationupregulation in oncogene in oncogene expression expression and anda downregulation a downregulation in tumor in tumor suppressor suppressor gene gene expressionexpression [9]. [9]. EpimutationEpimutation is characterized is characterized by a decrease by a in decrease the amount in the of amount global methylated of global methylated DNA DNA and an increaseand an in increase DNA methylation in DNA methylation in CpG (CG in CpGsite) islands, (CG site) a islands,region containing a region containing a huge a huge number ofnumber CpG dinucleotide of CpG dinucleotide repeats [10] repeats or regions [10] or of regions DNA ofwhere DNA a wherecytosine a cytosine nucleotide nucleotide is is followedfollowed by a guanine by a guanine in a linear in sequence a linear sequence of bases along of bases its along5′‐3′ direction. its 50-30 direction. CpG islands CpG islands are DNA aremethylation DNA methylation regions in regions promoters in promoters known to knownregulate to gene regulate expression gene expression through through transcriptionaltranscriptional silencing of silencing corresponding of corresponding genes [11]. genes CpG [islands11]. CpG usually islands extend usually for extend 300– for 300– 3000 base 3000pairs base in mammalian pairs in mammalian genomes and genomes are located and are within located or withinclose to or approximately close to approximately 50% of human50% ofpromoters human promoters [12,13]. Generally, [12,13]. Generally, this area is this not area located is not in locatedthe gene in promoter, the gene promoter, and the CpGand island the CpG is not island usually is not methylated usually methylated [14]. One [of14 ].the One leading of the causes leading of causesbreast of breast cancer is ancancer increase is an in increase DNMT1 in activity, DNMT1 which activity, leads which to the leads alteration to the alterationin DNA methylation in DNA methylation patterns andpatterns the increase and the in increase DNA methylation in DNA methylation in CpG islands in CpG [15]. islands [15]. The naturalThe product natural compound product compound is known isas knowna valuable as a source valuable of sourcemedicines of medicines because because of its bioactivityof its bioactivity [16]. In addition [16]. In addition to having to havingan anticancer an anticancer activity, activity, the natural the natural product product com- compoundspounds also pose also an pose advantage an advantage as a drug as a drugdue to due their to theirgood good bioavailability bioavailability and thera and therapeutic‐ peutic activityactivity [16,17]. [16,17 The]. The natural natural product product compounds compounds such such as as epigallocatechin epigallocatechin-3-gallate‐3‐gallate (EGCG), (EGCG), catechin,catechin, and and quercetin quercetin exhibit exhibit a a plausible plausible activity activity as an inhibitor of DNMT1, resulting resulting in DNA demethylation,demethylation, whichwhich reactivates reactivates the the tumor tumor suppressor suppressor gene gene expression, expres‐ thereby sion, therebyreducing reducing the the cancer cancer cell cell growth growth rate rate [18 [18,19].,19]. Therefore, Therefore, developing developing drug can candidates‐ as didates asDNMT1 DNMT1 inhibitors inhibitors is is a a potential potential strategy strategy for for breast breast cancer cancer treatment. treatment. The in silicoThe method in silico or method computer or‐ computer-aidedaided drug discovery drug discoveryand development and development is a rapidly is a rapidly developingdeveloping field since field it reduces since itthe reduces cost and the development cost and development time in drug time development in drug development [20]. [20]. The molecular docking and dynamic simulations have been regularly
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